First of all, your ad groups should be tightly grouped. I have used many programs. However, one free one is Adwords Editor. It works pretty well once you understand how the Keyword Grouper engine works. It will take some tweaking, but it is worth it (because it's free).

thanks mate. Im looking for a program that you input a shitload of kws and it automatically organises them in groups (e.g. 50 groups of 20 kws) automatically. Any links? (I have adwords editor but not sure if it does what Im looking for!)

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